Chemistry 5.07 Problem Set #3 - Enzyme catalysis and kinetics
|
|
- Chester Gardner
- 5 years ago
- Views:
Transcription
1 Chemistry 5.07 Problem Set #3 - Enzyme catalysis and kinetics Problem 1. Interleukin 1 β (IL-1 β) has been implicated in the pathogenesis of acute chronic inflammatory diseases including septic shock, rheumatoid arthritis etc. IL-1 β must be processed from a propeptide (pro-il-1 β) form of 31 kda to the active form of 17.5 kda by a cysteine protease designated ICE, or interleukin converting enzyme. The cleavage of IL-1 β occurs between Asp116 and Ala117. ICE is a unique cysteine protease, but appears to use a similar mechanism to other cysteine proteases requiring a histidine and a cysteine for catalysis. To study the enzyme, Merck had to develop an assay. As you can imagine, assays with a protein such as IL-1 β is cumbersome, and thus they did a number of experiments using peptides to see if they could find an effective peptide analog(s) to report on the substrate specificity and cleavage efficiency. They initially tried to determine the binding specificity length on either side of the bond to be cleaved (Figure 1), as well as the optimized amino acid binding at each subsite (Figure 2). The cleaved bond is between P1 and P1 (see Figure 1A, right) with aspartate at P1 (see Figure 1B), very important for cleavage. The assay required monitoring the reaction by HPLC where the peptide substrates and products needed to be separated and quantitated as a function of time. This assay is very slow and not very sensitive. Amino-terminal truncations Peptide Relative P7 P6 P5 P4 P3 P2 P1 P1' P2' P3' P4' P5' P6' P7' V max / K m 1 Asn Glu Ala Tyr Val His Asp Ala Pro Val Arg Ser Leu Asn 1.00 ± Glu Ala Tyr Val His Asp Ala Pro Val Arg Ser Leu Asn 0.64 ± Ala Tyr Val His Asp Ala Pro Val Arg Ser Leu Asn 0.29 ± Tyr Val His Asp Ala Pro Val Arg Ser Leu Asn 0.12 ± Ac-Tyr Val His Asp Ala Pro Val Arg Ser Leu Asn 0.81 ± Ac-Val His Asp Ala Pro Val Arg Ser Leu Asn < His Asp Ala Pro Val Arg Ser Leu Asn < Asp Ala Pro Val Arg Ser Leu Asn < Carboxy-terminal truncations Peptide Relative P7 P6 P5 P4 P3 P2 P1 P1' P2' P3' P4' P5' P6' P7' V max / K m 1 Asn Glu Ala Tyr Val His Asp Ala Pro Val Arg Ser Leu Asn 1.00 ± Asn Glu Ala Tyr Val His Asp Ala Pro Val Arg Ser Leu 1.22 ± Asn Glu Ala Tyr Val His Asp Ala Pro Val Arg Ser 0.80 ± Asn Glu Ala Tyr Val His Asp Ala Pro Val Arg 0.88 ± Asn Glu Ala Tyr Val His Asp Ala Pro Val 1.02 ± Asn Glu Ala Tyr Val His Asp Ala Pro 1.25 ± Asn Glu Ala Tyr Val His Asp Ala < Asn Glu Ala Tyr Val His Asp-CO-NH ± Ac-Tyr Val His Asp-NH-CH ± Ac-Tyr Val His Asp-AMC 1.9 ± 0.1 1
2 Figure 1 (previous page). Substrate specificity of Interleukin Converting Enzyme (ICE). A. Table of analogs of interleukin 1 (IL-1 ) used in assays to better understand the substrate specificity of ICE. B. Schematic of IL-1 with positions of P1, P2, P1, and P2 indicated and corresponding to amino acids listed in A. Table of analogs reprinted with permission from MacMillan Publishers Ltd: Nature Thornberry, Nancy A., Herbert G. Bull, Jimmy R. Calaycay, Kevin T. Chapman, Andrew D. Howard, Matthew J. Kostura, Douglas K. Miller et al. "A novel heterodimeric cysteine protease is required for interleukin-1βprocessing in monocytes." Nature 356, no (1992): Taking advantage of information gained by the studies in Figure 1, they then turned to develop a more high throughput (HTP), sensitive, assay using coumarin analogs, which upon peptide bond hydrolysis, become highly fluorescent. Thus the reaction could be monitored continuously in a spectrofluorometer. Alternatively, they used p-nitroanilide in place of the coumarin (see structure below). Using this assay they looked further at the substrate specificity and the results are reported in Figure 2 (below). Comparison of fluorogenic substrates for ICE Substrate 10-5 x k cat / K m' (M -1 s -1 ) Ac-WEHD-AMC 33.4 ± 0.3 Ac-WVHD-AMC 15.7 ± 0.1 Ac-YEHD-AMC 9.56 ± 0.20 Ac-WEAD-AMC 7.55 ± 0.07 Ac-YVHD-AMC 2.81 ± 0.14 Ac-WVAD-AMC 2.41 ± 0.60 Ac-YEAD-AMC 1.85 ± 0.07 Ac-YVAD-AMC 0.66 ± 0.14 pro-il-1 β 1.5 Figure 2. Examining the substrate specificity of Interleukin Converting Enzyme (ICE) using a coumarin fluorescence assay. A. Chemical structures of fluorescent coumarin substrates. B. Results of ICE activity in coumarin fluorescence assays using the substrates shown in A. Courtesy of Elsevier, Inc., Used with permission. Source: Rano, Thomas A., Tracy Timkey, Erin P. Peterson, Jennifer Rotonda, Donald W. Nicholson, Joseph W. Becker, Kevin T. Chapman, and Nancy A. Thornberry. "A combinatorial approach for determining protease specificities: application to interleukin-1β converting enzyme (ICE)." Chemistry & biology 4, no. 2 (1997):
3 The mechanism of cysteine proteases is proposed to be similar to serine proteases that you have or will be discussing in recitation (Figure 3). Figure 3. Schematic of a generic mechanism for serine proteases. These proteins have a catalytic triad, a coordinated catalytic pocket consisting of His at position 57, Ser at position 195 and Asp at position 102 of the polypeptide chain. Though distant in the primary structure of the protein, these residues are in close proximity in the quaternary structure as shown. However with cysteine proteases we know now from crystallographic studies and studies with many covalent inhibitors of cysteine proteases, that there are only two amino acids that play an essential role in catalysis: a cysteine and a histidine. Questions: a. What does the data in Figure 1 tell you about the substrate binding site to ICE? How does the k cat /K m or (V max / K m ) for the real substrate pro-il-1β meet your expectations relative to the other data? Explain why? b. Explain why the investigators decided to use the substrate analogs shown in Figure 2 to continue their substrate specificity studies. Can you think of how a more informative assay could be carried out? How would the corresponding p-nitroanilide analogs function in the assay? What criteria would you use to determine if the coumarin or the nitroanilide would be best for high throughput assays? c. Explain why k cat /K m is the kinetic parameter used in the studies described in Figure 1 and not k cat. d. Using the mechanism shown in Figure 3 for serine proteases, draw a corresponding mechanism for cysteine proteases. Based on what you have learned about serine proteases and the chemical difficulties associated with catalysis, provide an explanation for why an aspartate residue is not found in the active sites of cysteine proteases. 3
4 e. Peptide bond hydrolysis catalyzed by the enzyme is still x that of the non-enzymatic reaction. Discuss the different mechanisms of catalysis and their contributions to this rate acceleration. Problem 2. As with serine proteases, a number of different successful approaches have been achieved to target cysteine proteases once their specificity is understood. Shown below are two distinct approaches to inhibit cysteine proteases in general. The data below is shown for inhibition of ICE. The first is peptide aldehyde analogs where R in Figure 4 is replaced by an aldehyde (CHO). The second type of inhibitor is acyloxymethyl ketone analogs shown in Figure 5AB. Figure 4. Peptide aldehyde analogs of substrates for serine proteases. A. Chemical structure of a prototypical peptide aldehyde inhibitor with the R group representing the variable side chain. B. Chemical structure of an R group for a peptide aldehyde inhibitor. In this case, the R group is an aldehyde and has an inhibition constant of 0.76 nm. American Chemical Society. All right reserved. This content is excluded from our Creative Commons license. For more information, see 4
5 C. Figure 5. Inactivation of ICE by peptide (acyloxy) methyl (AMC) ketones. A. Chemical structure of a prototypical AMC ketone analogs. The variable side chain is represented by the R group. B. Table of possible R groups of the peptide AMC ketone analogs. C. Graph of reaction rates in the presence or absence of the AMC analogs listed in B. American Chemical Society. All right reserved. This content is excluded from our Creative Commons license. For more information, see Questions: a. Propose a mechanism of inhibition of ICE by the peptide aldehydes such as the one shown in Figure 4. This is a mechanism-based inhibitor. What type of inhibition would you expect to see using substrates in Figure 2 to analyze for inhibition? Show the equation and the kinetic reciprocal plots (1 v vs I [S\ ) with varying concentrations of substrate and inhibitor. b. From a chemical perspective, provide two reasons why you might not want to use an aldehyde as a therapeutic. c. The acyloxymethylketone analogs shown in Figure 5AB with the data shown in Figure 5C, have a mechanism of inhibition distinct from the peptide aldehydes. Propose a chemical mechanism for their inhibition of ICE. Provide an explanation for the data in Figure 5C. 5
6 MIT OpenCourseWare SC Biological Chemistry I Fall 2013 For information about citing these materials or our Terms of Use, visit:
Fig 1. Analogs to better understanding the substrate specificity of ICE
ANSWERS Problem Set 3 Enzyme catalysis and kinetics Problem 1. Interleukin 1 β (IL-1 β) has been implicated in the pathogenesis of acute chronic inflammatory diseases including septic shock, rheumatoid
More informationBC 367, Exam 2 November 13, Part I. Multiple Choice (3 pts each)- Please circle the single best answer.
Name BC 367, Exam 2 November 13, 2008 Part I. Multiple Choice (3 pts each)- Please circle the single best answer. 1. The enzyme pyruvate dehydrogenase catalyzes the following reaction. What kind of enzyme
More informationCase 7 A Storage Protein From Seeds of Brassica nigra is a Serine Protease Inhibitor
Case 7 A Storage Protein From Seeds of Brassica nigra is a Serine Protease Inhibitor Focus concept Purification of a novel seed storage protein allows sequence analysis and determination of the protein
More information466 Asn (N) to Ala (A) Generate beta dimer Interface
Table S1: Amino acid changes to the HexA α-subunit to convert the dimer interface from α to β and to introduce the putative GM2A binding surface from β- onto the α- subunit Residue position (α-numbering)
More informationCase 7 A Storage Protein From Seeds of Brassica nigra is a Serine Protease Inhibitor Last modified 29 September 2005
Case 7 A Storage Protein From Seeds of Brassica nigra is a Serine Protease Inhibitor Last modified 9 September 005 Focus concept Purification of a novel seed storage protein allows sequence analysis and
More informationBasic concepts of molecular biology
Basic concepts of molecular biology Gabriella Trucco Email: gabriella.trucco@unimi.it Life The main actors in the chemistry of life are molecules called proteins nucleic acids Proteins: many different
More informationFirst&year&tutorial&in&Chemical&Biology&(amino&acids,&peptide&and&proteins)&! 1.&!
First&year&tutorial&in&Chemical&Biology&(amino&acids,&peptide&and&proteins& 1.& a. b. c. d. e. 2.& a. b. c. d. e. f. & UsingtheCahn Ingold Prelogsystem,assignstereochemicaldescriptorstothe threeaminoacidsshownbelow.
More informationSerine Proteases and their Inhibitors
ugo Kubinyi, www.kubinyi.de Serine Proteases and their Inhibitors ugo Kubinyi Germany E-Mail kubinyi@t-online.de omepage www.kubinyi.de ugo Kubinyi, www.kubinyi.de Serine Proteases of Physiological Importance
More informationLecture 22: Questions from Quiz 2 and the Trypsin Digestion Experiment
Biological Chemistry Laboratory Biology 3515/Chemistry 3515 Spring 2018 Lecture 22: Questions from Quiz 2 and the Trypsin Digestion Experiment 29 March 2018 c David P. Goldenberg University of Utah goldenberg@biology.utah.edu
More informationBio 451 Examination I September 22, 1995
Bio 451 Examination I September 22, 1995 PLEASE PRINT YOUR NAME CLEARLY ON EVERY PAGE OF THIS EXAMINATION; IF THIS IS NOT DONE, WE WILL SET YOUR EXAM ASIDE WHEN THE EXAMS ARE TAKEN APART FOR GRADING. Answer
More informationTurning λ Cro into a
Turning λ Cro into a 3 Transcriptional Activator Figure by MIT pencourseware. Fred Bushman and Mark Ptashne Cell (1988) 54:191-197 Presented by atalie Kuldell for 0.90 February 4th, 009 Small patch of
More informationProblem Set Unit The base ratios in the DNA and RNA for an onion (Allium cepa) are given below.
Problem Set Unit 3 Name 1. Which molecule is found in both DNA and RNA? A. Ribose B. Uracil C. Phosphate D. Amino acid 2. Which molecules form the nucleotide marked in the diagram? A. phosphate, deoxyribose
More information6 Enzymes II W. H. Freeman and Company
6 Enzymes II 2017 W. H. Freeman and Company The role of an enzyme in an enzyme-catalyzed reaction is to: A. bind a transition state intermediate, such that it cannot be converted back to substrate. B.
More informationProblem: The GC base pairs are more stable than AT base pairs. Why? 5. Triple-stranded DNA was first observed in 1957. Scientists later discovered that the formation of triplestranded DNA involves a type
More informationZool 3200: Cell Biology Exam 3 3/6/15
Name: Trask Zool 3200: Cell Biology Exam 3 3/6/15 Answer each of the following questions in the space provided; circle the correct answer or answers for each multiple choice question and circle either
More information蛋白質體學. Proteomics Amino acids, Peptides and Proteins 陳威戎 & 21
蛋白質體學 Proteomics 2015 Amino acids, Peptides and Proteins 陳威戎 2015. 09. 14 & 21 Outline 1. Amino Acids 2. Peptides and Proteins 3. Covalent Structure of Proteins Amino Acids Proteins are polymers of amino
More informationBasic concepts of molecular biology
Basic concepts of molecular biology Gabriella Trucco Email: gabriella.trucco@unimi.it What is life made of? 1665: Robert Hooke discovered that organisms are composed of individual compartments called cells
More informationProtein Structure/Function Relationships
Protein Structure/Function Relationships W. M. Grogan, Ph.D. OBJECTIVES 1. Describe and cite examples of fibrous and globular proteins. 2. Describe typical tertiary structural motifs found in proteins.
More informationi. Monomers for which class(s) of macromolecules always have phosphorous? Circle all that apply. Carbohydrates Proteins Lipids DNA RNA
Question 1 (25 points) a) There are four major classes of biological macromolecules: carbohydrates, proteins, lipids and nucleic acids (deoxyribonucleic acid or DNA and ribonucleic acid or RNA). i. Monomers
More informationExperimental Design. Margaret A. Daugherty. Fall Michaelis Menton Kinetics and Inhibition. Lecture 14: Enzymes & Kinetics III E + S ES E + P
Lecture 14: Enzymes & Kinetics III Michaelis Menton Kinetics and Inhibition Margaret A. Daugherty Fall 2003 Experimental Design k 1 k cat E + S ES E + P k -1 I want to measure the reactivity of my enzyme
More informationSolutions to Problem Set 1
MIT Department of Biology 7.014 Introductory Biology, Spring 004 Question 1 Solutions to 7.014 Problem Set 1 a) Describe the conditions of the atmosphere on prebiotic earth and how these conditions differ
More information6-Foot Mini Toober Activity
Big Idea The interaction between the substrate and enzyme is highly specific. Even a slight change in shape of either the substrate or the enzyme may alter the efficient and selective ability of the enzyme
More informationPurification: Step 1. Lecture 11 Protein and Peptide Chemistry. Cells: Break them open! Crude Extract
Purification: Step 1 Lecture 11 Protein and Peptide Chemistry Cells: Break them open! Crude Extract Total contents of cell Margaret A. Daugherty Fall 2003 Big Problem: Crude extract is not the natural
More informationPurification: Step 1. Protein and Peptide Chemistry. Lecture 11. Big Problem: Crude extract is not the natural environment. Cells: Break them open!
Lecture 11 Protein and Peptide Chemistry Margaret A. Daugherty Fall 2003 Purification: Step 1 Cells: Break them open! Crude Extract Total contents of cell Big Problem: Crude extract is not the natural
More informationBi Lecture 3 Loss-of-function (Ch. 4A) Monday, April 8, 13
Bi190-2013 Lecture 3 Loss-of-function (Ch. 4A) Infer Gene activity from type of allele Loss-of-Function alleles are Gold Standard If organism deficient in gene A fails to accomplish process B, then gene
More informationSUMMARY OF DOCTORAL DISSARTATION
Monika Łęgowska Katedra Biochemii Nr indeksu: 2541 SUMMARY OF DOCTORAL DISSARTATION In search of substrates and inhibitors of human cathepsin C. Design, chemical synthesis and biological studies Cathepsin
More informationSUPPLEMENTARY INFORMATION Figures. Supplementary Figure 1 a. Page 1 of 30. Nature Chemical Biology: doi: /nchembio.2528
SUPPLEMENTARY INFORMATION Figures Supplementary Figure 1 a b c Page 1 of 0 11 Supplementary Figure 1: Biochemical characterisation and binding validation of the reversible USP inhibitor 1. a, Biochemical
More information2018 Protein Modeling Exam Key
2018 Protein Modeling Exam Key Multiple Choice: 1. Which of the following amino acids has a negative charge at ph 7? a. Gln b. Glu c. Ser d. Cys 2. Which of the following is an example of secondary structure?
More informationFrom mechanism to medicne
From mechanism to medicne a look at proteins and drug design Chem 342 δ δ δ+ M 2009 δ+ δ+ δ M Drug Design - an Iterative Approach @ DSU Structural Analysis of Receptor Structural Analysis of Ligand-Receptor
More informationLaboratory Evolution of Robust and Enantioselective Baeyer-Villiger Monooxygenases for Asymmetric Catalysis
Laboratory Evolution of Robust and Enantioselective Baeyer-Villiger Monooxygenases for Asymmetric Catalysis Induced fit docking model Manfred T. Reetz* and Sheng Wu Max-Planck-Institut für Kohlenforschung
More informationAmino Acids and Proteins
Various Functions of Proteins SB203 Amino Acids and Proteins Jirundon Yuvaniyama, Ph.D. Department of Biochemistry Faculty of Science Mahidol University Enzymes Transport proteins utrient and storage proteins
More information11 questions for a total of 120 points
Your Name: BYS 201, Final Exam, May 3, 2010 11 questions for a total of 120 points 1. 25 points Take a close look at these tables of amino acids. Some of them are hydrophilic, some hydrophobic, some positive
More informationSensoLyte 440 West Nile Virus Protease Assay Kit *Fluorimetric*
SensoLyte 440 West Nile Virus Protease Assay Kit *Fluorimetric* Revision Number: 1.1 Last updated: October 2014 Catalog # Kit Size AS-72079 500 Assays (96-well) Optimized Performance: This kit is optimized
More informationBioinformatics. ONE Introduction to Biology. Sami Khuri Department of Computer Science San José State University Biology/CS 123A Fall 2012
Bioinformatics ONE Introduction to Biology Sami Khuri Department of Computer Science San José State University Biology/CS 123A Fall 2012 Biology Review DNA RNA Proteins Central Dogma Transcription Translation
More informationIn silico measurements of twist and bend. moduli for beta solenoid protein self-
In silico measurements of twist and bend moduli for beta solenoid protein self- assembly units Leonard P. Heinz, Krishnakumar M. Ravikumar, and Daniel L. Cox Department of Physics and Institute for Complex
More informationUnit 1. DNA and the Genome
Unit 1 DNA and the Genome Gene Expression Key Area 3 Vocabulary 1: Transcription Translation Phenotype RNA (mrna, trna, rrna) Codon Anticodon Ribosome RNA polymerase RNA splicing Introns Extrons Gene Expression
More informationDr. R. Sankar, BSE 631 (2018)
Pauling, Corey and Branson Diffraction of DNA http://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050 In short, stereochemistry is important in determining which helices
More informationEach enzyme has a unique 3-D shape and recognizes and binds only the specific substrate of a reaction.
1 Enzyme = protein molecule that serves as a biological catalyst. allow life to go on. speed up and regulate metabolic reactions. Catalyst= a chemical that speeds up the rate of a reaction without itself
More informationNanobiotechnology. Place: IOP 1 st Meeting Room Time: 9:30-12:00. Reference: Review Papers. Grade: 50% midterm, 50% final.
Nanobiotechnology Place: IOP 1 st Meeting Room Time: 9:30-12:00 Reference: Review Papers Grade: 50% midterm, 50% final Midterm: 5/15 History Atom Earth, Air, Water Fire SEM: 20-40 nm Silver 66.2% Gold
More informationSensoLyte 490 MMP-3 Assay Kit *Fluorimetric*
SensoLyte 490 MMP-3 Assay Kit *Fluorimetric* Revision Number:1.1 Last Revised: October 2014 Catalog # Kit Size AS-71130 500 assays (96-well) Convenient Format: All essential assay components are included.
More informationFundamentals of Protein Structure
Outline Fundamentals of Protein Structure Yu (Julie) Chen and Thomas Funkhouser Princeton University CS597A, Fall 2005 Protein structure Primary Secondary Tertiary Quaternary Forces and factors Levels
More informationSensoLyte 520 MMP-1 Assay Kit *Fluorimetric*
SensoLyte 520 MMP-1 Assay Kit *Fluorimetric* Revision# 1.2 Last Updated: February 2017 Catalog # Kit Size AS-71150 100 Assays (96-well) or 250 Assays (384-well) Convenient Format: All essential assay components
More informationRenin Inhibitor Screening Assay Kit
Renin Inhibitor Screening Assay Kit Catalog Number KA1361 96 assays Version: 02 Intended for research use only www.abnova.com Table of Contents Introduction... 3 Background... 3 Principle of the Assay...
More informationMOLEBIO LAB #3: Electrophoretic Separation of Proteins
MOLEBIO LAB #3: Electrophoretic Separation of Proteins Introduction: Proteins occupy a central position in the structure and function of all living organisms. Some proteins serve as structural components
More informationAli Yaghi. Tamara Wahbeh. Mamoun Ahram
28 Ali Yaghi Tamara Wahbeh Mamoun Ahram This sheet is a continuation of protein purification methods. Isoelectric focusing Separation of proteins based on Isoelectric points(charge),and it is a horizontal
More informationCHROMOGENIC SUBSTRATE TECHNOLOGY. Giovanni Russi
CHROMOGENIC SUBSTRATE TECHNOLOGY Giovanni Russi What is a chromogenic substrate? A peptide linked to a chromophore The peptide is formed by 3-5 residues The chromophore is p-nitroaniline (p-na) The residues
More informationAddison Ault, Department of Chemistry, Cornell College, Mount Vernon, IA. The isoelectric point is a point on the ph scale. It is the ph at which the
1 Isoelectric Points On the Back of the Envelope Addison Ault, Department of Chemistry, Cornell College, Mount Vernon, IA The isoelectric point is a point on the ph scale. It is the ph at which the average
More informationNucleic acid and protein Flow of genetic information
Nucleic acid and protein Flow of genetic information References: Glick, BR and JJ Pasternak, 2003, Molecular Biotechnology: Principles and Applications of Recombinant DNA, ASM Press, Washington DC, pages.
More informationSpecificity of Proteolysis
Borivoj Keil Specificity of Proteolysis With 17 Figures and 20 Tables Springer-Verlag Berlin Heidelberg New York London Paris Tokyo Hong Kong Barcelona Budapest Prof. Dr. Borivoj Keil Institut Pasteur
More informationSensoLyte 490 MMP-1 Assay Kit *Fluorimetric*
SensoLyte 490 MMP-1 Assay Kit *Fluorimetric* Revision# 1.2 Last updated: February 2017 Catalog # Kit Size AS-71128 500 Assays (96-well plate) or 1250 assays (384-well) Convenient Format: All essential
More informationProteins Amides from Amino Acids
Chapter 26 and Chapter 28 Proteins Amides from Amino Acids Amino acids contain a basic amino group and an acidic carboxyl group Joined as amides between the ¾NH 2 of one amino acid and the ¾CO 2 H to the
More informationScanning the Prime-Site Substrate Specificity of Proteolytic Enzymes: A Novel Assay Based on Ligand-Enhanced Lanthanide Ion Fluorescence
Bioorganic & Medicinal Chemistry Letters 12 (2002) 3619 3623 Scanning the Prime-Site Substrate Specificity of Proteolytic Enzymes: A Novel Assay Based on Ligand-Enhanced Lanthanide Ion Fluorescence Amy
More informationProtein Structure and Function! Lecture 4: ph, pka and pi!
Protein Structure and Function! Lecture 4: ph, pka and pi! Definition of ph and pk a! ph is a measure of the concentration of H +.! + ph = log 10[H ] For a weak acid,! HA #!!"! H + + A!, K a = [H + ][A!
More informationAlgorithms in Bioinformatics ONE Transcription Translation
Algorithms in Bioinformatics ONE Transcription Translation Sami Khuri Department of Computer Science San José State University sami.khuri@sjsu.edu Biology Review DNA RNA Proteins Central Dogma Transcription
More informationSupporting Information
Supporting Information A Facile and Sensitive Near-Infrared Fluorescence Probe for the Detection of Endogenous Alkaline Phosphatase Activity in Vivo Song-Jiao Li, Chun-Yan Li,*,, Yong-Fei Li, Junjie Fei,
More informationProgramme Good morning and summary of last week Levels of Protein Structure - I Levels of Protein Structure - II
Programme 8.00-8.10 Good morning and summary of last week 8.10-8.30 Levels of Protein Structure - I 8.30-9.00 Levels of Protein Structure - II 9.00-9.15 Break 9.15-11.15 Exercise: Building a protein model
More informationCustom [ 125 I] Radioiodination
Page 1 Custom [ 125 I] Radioiodination Radioiodination of proteins and peptides may be performed by different methods, namely by targeting an iodine-accepting group on the protein or by the conjugation
More informationExamination I PHRM 836 Biochemistry for Pharmaceutical Sciences II September 29, 2015
Examination I PHRM 836 Biochemistry for Pharmaceutical Sciences II September 29, 2015 PHRM 836 Exam I - 1 Name: Instructions 1. Check your exam to make certain that it has 9 pages including this cover
More informationab MMP14 Inhibitor Screening Assay Kit (Colorimetric)
ab139454 MMP14 Inhibitor Screening Assay Kit (Colorimetric) Instructions for Use For the screening of MMP14 inhibitors This product is for research use only and is not intended for diagnostic use. Version
More information36. The double bonds in naturally-occuring fatty acids are usually isomers. A. cis B. trans C. both cis and trans D. D- E. L-
36. The double bonds in naturally-occuring fatty acids are usually isomers. A. cis B. trans C. both cis and trans D. D- E. L- 37. The essential fatty acids are A. palmitic acid B. linoleic acid C. linolenic
More informationEE550 Computational Biology
EE550 Computational Biology Week 1 Course Notes Instructor: Bilge Karaçalı, PhD Syllabus Schedule : Thursday 13:30, 14:30, 15:30 Text : Paul G. Higgs, Teresa K. Attwood, Bioinformatics and Molecular Evolution,
More informationSensoLyte Homogeneous AFC Caspase-8 Assay Kit *Fluorimetric*
SensoLyte Homogeneous AFC Caspase-8 Assay Kit *Fluorimetric* Catalog # 72088-100 Kit Size 100 Assays (96-well plate) Optimized Performance: This kit is optimized to detect caspase-8 activity. Enhanced
More informationDr. Jeffrey P. Thompson bio350
Chapter 8 Enzymes Green light GFP Blue light Modern day catalysis Catalysis (reaction promotion) may have gotten its beginning g in an RNA- dominated world. Most catalysis today has evolved into using
More informationCristian Micheletti SISSA (Trieste)
Cristian Micheletti SISSA (Trieste) michelet@sissa.it Mar 2009 5pal - parvalbumin Calcium-binding protein HEADER CALCIUM-BINDING PROTEIN 25-SEP-91 5PAL 5PAL 2 COMPND PARVALBUMIN (ALPHA LINEAGE) 5PAL 3
More informationBi 8 Lecture 7. Ellen Rothenberg 26 January Reading: Ch. 3, pp ; panel 3-1
Bi 8 Lecture 7 PROTEIN STRUCTURE, Functional analysis, and evolution Ellen Rothenberg 26 January 2016 Reading: Ch. 3, pp. 109-134; panel 3-1 (end with free amine) aromatic, hydrophobic small, hydrophilic
More informationSensoLyte Homogeneous AFC Caspase-3/7 Assay Kit
SensoLyte Homogeneous AFC Caspase-3/7 Assay Kit Catalog # 71114 Unit Size Kit Size 1 Kit 500 Assays (96-well) or 1250 Assays (384-well) This kit is optimized to detect caspase-3/7 activity in cell culture
More information7.014 Solution Set 4
7.014 Solution Set 4 Question 1 Shown below is a fragment of the sequence of a hypothetical bacterial gene. This gene encodes production of HWDWN, protein essential for metabolizing sugar yummose. The
More informationAbbreviations. Inhibitor synthesis
Supplementary Material I for: Bailey et al. manuscript An analysis of subdomain orientation, conformational change and disorder in relation to crystal packing of aspartic proteinases. Abbreviations Boc
More informationCh Biophysical Chemistry
Ch 247.53. Biophysical Chemistry Nina Rosario L. Rojas 2012-2013 sem 1 Review of Protein Structure Why structure? Primary, secondary, tertiary structure Disulfide bonds scheme 2 STRUCTURE- REGULAR STRUCTURE
More informationN. GOOD NUCLEASE/BAD NUCLEASE
N. GOOD NUCLEASE/BAD NUCLEASE Background Figure N.1. Simplified scheme for the general acid/base-catalyzed hydrolysis of RNA. A pentavalent intermediate is formed along the pathway. The hydrolysis of RNA
More informationExamination I PHRM 836 Biochemistry for Pharmaceutical Sciences II September 29, 2015
Examination I PHRM 836 Biochemistry for Pharmaceutical Sciences II September 29, 2015 PHRM 836 Exam I - 1 Name: Instructions 1. Check your exam to make certain that it has 9 pages including this cover
More informationEnzymes Part III: regulation I. Dr. Mamoun Ahram Summer, 2017
Enzymes Part III: regulation I Dr. Mamoun Ahram Summer, 2017 Mechanisms of regulation Expression of isoenzymes Regulation of enzymatic activity Inhibitors Conformational changes Allostery Modulators Reversible
More informationAmino Acid Sequences and Evolutionary Relationships
Amino Acid Sequences and Evolutionary Relationships One technique used to determine evolutionary relationships is to study the biochemical similarity of organisms. Though molds, aardvarks, and humans appear
More informationChapter Twelve Protein Synthesis: Translation of the Genetic Message
Mary K. Campbell Shawn O. Farrell international.cengage.com/ Chapter Twelve Protein Synthesis: Translation of the Genetic Message Paul D. Adams University of Arkansas 1 Translating the Genetic Message
More informationZ -LYTE fluorescent kinase assay technology. Z -LYTE Kinase Assay Platform
Z -LYTE fluorescent kinase assay technology Z -LYTE Kinase Assay Platform Z -LYTE Kinase Assay Platform Non-radioactive assay format for screening a diverse collection of over 185 kinase targets Assay
More informationCambridge International Examinations Cambridge International Advanced Subsidiary and Advanced Level
Cambridge International Examinations Cambridge International Advanced Subsidiary and Advanced Level *2249654089* BIOLOGY 9700/21 Paper 2 AS Level Structured Questions October/November 2016 1 hour 15 minutes
More informationSensoLyte Homogeneous Rh110 Caspase-3/7 Assay Kit
SensoLyte Homogeneous Rh110 Caspase-3/7 Assay Kit Catalog # 71141 Unit Size Kit Size 1 Kit 500 Assays (96-well) or 1250 Assays (384-well) This kit is optimized to detect caspase-3/7 activity in cell culture
More informationSolutions to 7.02 Quiz II 10/27/05
Solutions to 7.02 Quiz II 10/27/05 Class Average = 83 Standard Deviation = 9 Range Grade % 87-100 A 43 74-86 B 39 55-73 C 17 > 54 D 1 Question 1 (56 points) While studying deep sea bacteria, you discover
More informationSupporting Information. Electrochemiluminescence Peptide-Based Biosensor with Hetero-
Supporting Information Electrochemiluminescence Peptide-Based Biosensor with Hetero- Nanostructures as Co-reaction Accelerator for the Ultra-sensitive Determination of Tryptase Fang-Fang Wu, Ying Zhou,
More informationMaterials Protein synthesis kit. This kit consists of 24 amino acids, 24 transfer RNAs, four messenger RNAs and one ribosome (see below).
Protein Synthesis Instructions The purpose of today s lab is to: Understand how a cell manufactures proteins from amino acids, using information stored in the genetic code. Assemble models of four very
More informationProtein sorting at surfaces: Parallel affinity capture to patterns
Protein sorting at surfaces: Parallel affinity capture to patterns Fang Cheng, Manish Dubey, Lara Gamble, David Castner University of Washington, USA Hironobu Takahashi, Fang Liu, Greg Harbers, David Grainger
More informationStructure Based Virtual Screening for Discovery of Novel Human Neutrophil Elastase Inhibitors
Structure Based Virtual Screening for Discovery of Novel Human Neutrophil Elastase Inhibitors Susana D. Lucas, a Lídia M. Gonçalves, a Teresa A. F. Cardote, a Henrique F. Correia, a Rui Moreira, a Rita
More informationSpeaker: Yu-Chen Ku Professor: Ching-Tsan Huang, Ph. D. Source: Biochemical Journal (2007) 402, Date: December 4th, 2007
Directed evolution and structural analysis of N-carbamoyl-D-amino acid amidohydrolase provide insights into recombinant protein solubility in Escherichia coli Speaker: Yu-Chen Ku Professor: Ching-Tsan
More informationFrom code to translation
From code to translation What could be the role of the first peptides? Ádám Kun & Ádám Radványi Dpt. Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary Parmenides
More informationStructure formation and association of biomolecules. Prof. Dr. Martin Zacharias Lehrstuhl für Molekulardynamik (T38) Technische Universität München
Structure formation and association of biomolecules Prof. Dr. Martin Zacharias Lehrstuhl für Molekulardynamik (T38) Technische Universität München Motivation Many biomolecules are chemically synthesized
More informationStudy of Nisin and Sublancin:
Study of Nisin and Sublancin: A Strategy for Protection of the United States Food Supply from Pathogenic Bacterial Spores Introduced through Bioterrorism JIFSAN Project November, 2004 J. Norman Hansen,
More informationSensoLyte 490 MMP-9 Assay Kit *Fluorimetric*
SensoLyte 490 MMP-9 Assay Kit *Fluorimetric* Revision#1.2 Last updated: February 2017 Catalog # Kit Size AS-71134 500 assays (96-well) or 1250 assays (384-well) Convenient Format: All essential assay components
More informationSensoLyte 520 MMP Substrate Sampler Kit *Fluorimetric*
SensoLyte 520 MMP Substrate Sampler Kit *Fluorimetric* Catalog # 71170 Kit Size 16 X 20 assays Convenient Format: All essential assay components are included. Optimized Performance: Optimal conditions
More information7.013 Problem Set 3 FRIDAY October 8th, 2004
MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert. Weinberg, Dr. laudette ardel Name: T: 7.013 Problem Set 3 FRIDY October 8th, 2004 Problem
More informationEnzyme kinetics. Irreversible inhibition inhibitor is bound tightly to enzyme - very slow dissociation can be covalent or non covalently bound
Enzymes can be regulated by acceleration and inhibition inhibition very common - several different mechanisms competitive / non competitive reversible / irreversible Irreversible inhibition inhibitor is
More informationSensoLyte Homogeneous AFC Caspase-8 Assay Kit *Fluorimetric*
SensoLyte Homogeneous AFC Caspase-8 Assay Kit *Fluorimetric* Catalog # 7288-2 Kit Size 2 Assays (96-well plate) Optimized Performance: This kit is optimized to detect caspase-8 activity. Enhanced Value:
More informationPhosphoserine-rich Protein from Phragmatopoma californica. Leila Jirari Mentor: Chengjun Sun Herbert Waite NIH, NSF, NASA
Phosphoserine-rich Protein from Phragmatopoma californica Leila Jirari Mentor: Chengjun Sun Herbert Waite NIH, NSF, NASA Why Study This Worm? Underwater adhesive Glue adheres to eggs shells, glass, teeth
More informationProtein analysis. Dr. Mamoun Ahram Summer semester, Resources This lecture Campbell and Farrell s Biochemistry, Chapters 5
Protein analysis Dr. Mamoun Ahram Summer semester, 2015-2016 Resources This lecture Campbell and Farrell s Biochemistry, Chapters 5 Bases of protein separation Proteins can be purified on the basis Solubility
More informationAmino Acid Sequences and Evolutionary Relationships
Amino Acid Sequences and Evolutionary Relationships Pre-Lab Discussion Homologous structures -- those structures believed to have a common origin but not necessarily a common function -- provide some of
More informationSTRUCTURAL BIOLOGY. α/β structures Closed barrels Open twisted sheets Horseshoe folds
STRUCTURAL BIOLOGY α/β structures Closed barrels Open twisted sheets Horseshoe folds The α/β domains Most frequent domain structures are α/β domains: A central parallel or mixed β sheet Surrounded by α
More informationActivation and specificity of Thrombin. Giulia Pavani
Activation and specificity of Thrombin Giulia Pavani Summary Regulation of a Serine Protease: Thrombin Zymogen Enzyme Substrate Specificity Staphylocoagulase Bacteria know how a protease works (much more
More informationIntroduction to Proteins
Introduction to Proteins Lecture 4 Module I: Molecular Structure & Metabolism Molecular Cell Biology Core Course (GSND5200) Matthew Neiditch - Room E450U ICPH matthew.neiditch@umdnj.edu What is a protein?
More information